MSIsensor for tumor-only

[jfnavarro]

It would be nice to add a process to compute MSIs for tumor-only samples:

https://github.com/niu-lab/msisensor2

I could take care of this.

[FriederikeHanssen]

Hi! i looked into this a bit, looks like you need to create a baseline form public data beforehand. To ensure this is all in the right container and reproducible etc, I think we would need a bit of a change of the input,...maybe allowing two inputs...? not sure..i would say we can maybe push this to 3.1

[SusiJo]

Hi! I started working on integrating the msisensor2 module into sarek, but unfortunantely it only takes bam as input.
So I opened an issue - maybe they can integrate cram input into msisensor2 in the future.